Novel Pipeline for Large-Scale Comparative Population Genetics

As scientists continue to ask complex questions about biodiversity and deal with increasingly large amounts of data, there is a demand for new methods and computational developments to perform scientific analyses. Analytical pipelines and modules can provide a way to meet these demands and ensure reproducibility in scientific methods and analyses. The goal of this study was to create efficient, reproducible, reusable programming modules that are publicly available for future research. These modules were used to determine population genetic structure measures and compare these measures across species with different biological traits. The functionality of the modules is shown through a case study on Diptera (true fly) species from Canada and Greenland. We leveraged high-throughput DNA sequencing data from Northern areas, as it is a valuable resource and provides new opportunities to study the Arctic. Data were pulled from public databases (Barcode of Life Data System and Global Biodiversity Information Facility), as well as taxon-specific literature. The pipeline we developed in R includes fifteen modules, including modules to prepare and filter the data, calculate population genetic structure measures (e.g., FST), and run a multiple regression. These modules can be easily adapted and applied to a diverse set of animal groups, geographic regions, and biological traits. Best practices were followed for pipeline development, and the modules were designed and tested to work for datasets of different sizes by providing multiple different analyses and filtering options. Biological results were also obtained for Diptera species. Habitat and larval diet were both significantly related to population genetic structure. Evidence of isolation by distance and a relationship between population genetic structure and both latitude and longitude were also found. Overall, this study has created efficient, reusable bioinformatics modules, and provided insight into the factors affecting population genetic structure in Northern fly communities.